AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images

About

Autofluorescence is a long-standing problem that has hindered fluorescence microscopy image analysis. To address this, we have developed a method that identifies autofluorescent signals from multi-channel images post acquisition. See the gallery for examples demonstrating the broad utility of this algorithm in accurately identifying and removing interfering autofluorescent signals. You can find more information on how our tool works here.

Software

For the benefit of the community we have made our autofluorescence identification tool and vignettes illustrating its use available for...

FIJI:     https://github.com/ellispatrick/AFidImageJ     [please use latest version of Fiji]
Matlab:     https://github.com/ellispatrick/AFidMatlab
R:     https://github.com/ellispatrick/AFidR

Citation

We very much appreciate you referencing our work when you use it.

Baharlou H*, Canete, N*, Bertram KM, Sandgren KJ, Cunningham AL, Harman AN and Patrick E. (2019) AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images bioarxiv
Raw data and scripts to reproduce the figures are available on https://zenodo.org/record/3898373#.Xuq-NkUvOUl